Where to put your blog? How about blog.domain.com? Putting your blog on a sub-domain makes it easy to keep all the files for your blog organized and separate from your other website files, you know, the CMS, the forum and the wiki you have jumbled on the site too. The sub-domain keeps all the links easy to manage too. But, with blog.domain.com, you may have an impact to you site ranking as Google sees a sub-domain as a separate site (as discussed in www or not, just make sure you canonicalize it). If you are worried about Google rankings, go with something like domain.com/blog.
Even without a sub-domain, you can keep things tidy. I usually structure my sites with a hierarchy of folders. I put all my web applications in individual folders at the same level to keep everything separate so you can blow away an application and replace it without messing up the others. If you install an application at the root you will have other installed application folders mixed in at it becomes much more of a challenge to upgrade/patch. With everything in a folder you can even install major upgrades in parallel with your existing site, do testing in parallel and simple rename folders when you are ready to switch.